Variant report

Variant	rs13077262
Chromosome Location	chr3:67705745-67705746
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:67703060-67706271	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:67705673-67706364	GM12892	blood:	n/a	n/a
3	NFYA	chr3:67705611-67706113	Hela-S3	cervix:	n/a	chr3:67705915-67705933 chr3:67705874-67705892
4	SP1	chr3:67705605-67706422	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:67705715-67706479	GM12892	blood:	n/a	n/a
6	NFYB	chr3:67705623-67706265	K562	blood:	n/a	chr3:67705985-67706000
7	NFYA	chr3:67705418-67706239	GM12878	blood:	n/a	chr3:67705915-67705933 chr3:67705874-67705892
8	POLR2A	chr3:67703934-67706381	GM12878	blood:	n/a	n/a
9	SP1	chr3:67705677-67706196	K562	blood:	n/a	n/a
10	POU2F2	chr3:67705715-67706588	GM12891	blood:	n/a	n/a
11	SP1	chr3:67705681-67706178	A549	lung:	n/a	n/a
12	NFYB	chr3:67705318-67706450	GM12878	blood:	n/a	chr3:67705985-67706000
13	FOXM1	chr3:67705717-67706635	GM12878	blood:	n/a	n/a
14	POU2F2	chr3:67705707-67706425	GM12878	blood:	n/a	n/a
15	NFYA	chr3:67705357-67706224	K562	blood:	n/a	chr3:67705915-67705933 chr3:67705874-67705892
16	SP1	chr3:67705488-67706466	GM12878	blood:	n/a	n/a
17	MAFF	chr3:67705744-67706079	HepG2	liver:	n/a	chr3:67705917-67705935 chr3:67705942-67705960
18	SP1	chr3:67705664-67706138	HepG2	liver:	n/a	n/a
19	MAFK	chr3:67705060-67706046	HepG2	liver:	n/a	chr3:67705918-67705933 chr3:67705943-67705958
20	NFIC	chr3:67705744-67706779	GM12878	blood:	n/a	n/a
21	SETDB1	chr3:67705714-67706378	U2OS	brain:	n/a	n/a
22	NFYB	chr3:67705608-67706257	Hela-S3	cervix:	n/a	chr3:67705985-67706000
23	POLR2A	chr3:67704299-67706188	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:67697874..67699560-chr3:67705440..67708186,2	K562	blood:

Variant related genes	Relation type
SUCLG2	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11707967	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11712921	0.85[EUR][1000 genomes]
rs11717561	0.85[EUR][1000 genomes]
rs11719952	0.87[EUR][1000 genomes]
rs12714500	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13065696	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13068759	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13068996	0.84[EUR][1000 genomes]
rs13069212	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13069251	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13070332	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13076100	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13081838	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083820	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13086260	0.85[EUR][1000 genomes]
rs13090197	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13091275	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13091330	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13092662	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13099253	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1376028	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1376029	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1376030	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1450345	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1473351	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1814519	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1823476	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2167181	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2198015	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2198016	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2218796	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2362453	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2362454	0.80[AMR][1000 genomes]
rs2362455	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62256429	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6548721	0.82[AFR][1000 genomes]
rs6766403	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770260	0.83[AFR][1000 genomes]
rs6774971	0.86[EUR][1000 genomes]
rs6778266	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6779395	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781799	0.83[AFR][1000 genomes]
rs6786211	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787200	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6787642	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6787853	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6788874	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790771	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6791337	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6793868	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6797010	0.86[EUR][1000 genomes]
rs6797460	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798228	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6806285	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6806536	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6808106	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71621318	0.84[EUR][1000 genomes]
rs7434004	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7610446	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7615766	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7632886	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7639427	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7647518	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7653350	0.82[EUR][1000 genomes]
rs881948	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs881949	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs935734	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9811187	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9824834	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3359258	chr3:67589615-67828274	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv876922	chr3:67635506-67755257	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv428739	chr3:67656829-67730379	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13077262	RP11-81N13.1	cis	Thyroid	GTEx
rs13077262	RP11-81N13.1	cis	lung	GTEx
rs13077262	SUCLG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67703400-67705800	Active TSS	NHLF	lung
2	chr3:67703600-67705800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:67703600-67706000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr3:67703600-67706000	Active TSS	A549	lung
5	chr3:67703600-67706400	Active TSS	Colonic Mucosa	Colon
6	chr3:67703600-67706400	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr3:67703800-67706000	Active TSS	Fetal Intestine Small	intestine
8	chr3:67704000-67705800	Active TSS	Fetal Intestine Large	intestine
9	chr3:67704000-67705800	Active TSS	Fetal Kidney	kidney
10	chr3:67704000-67705800	Active TSS	Psoas Muscle	Psoas
11	chr3:67704000-67705800	Active TSS	HSMMtube	muscle
12	chr3:67704000-67706000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:67704000-67706600	Active TSS	Brain Hippocampus Middle	brain
14	chr3:67704200-67705800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr3:67704200-67705800	Active TSS	Brain Substantia Nigra	brain
16	chr3:67704200-67705800	Active TSS	Left Ventricle	heart
17	chr3:67704200-67705800	Active TSS	Ovary	ovary
18	chr3:67704200-67706000	Active TSS	Lung	lung
19	chr3:67704200-67706000	Active TSS	NHDF-Ad	bronchial
20	chr3:67704400-67705800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:67704400-67705800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:67704400-67705800	Active TSS	Placenta Amnion	Placenta Amnion
23	chr3:67704400-67705800	Active TSS	HepG2	liver
24	chr3:67704400-67705800	Active TSS	HSMM	muscle
25	chr3:67704400-67706200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:67704400-67706200	Active TSS	Colon Smooth Muscle	Colon
27	chr3:67704400-67706400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:67704400-67706400	Active TSS	Brain Anterior Caudate	brain
29	chr3:67704400-67706600	Active TSS	Rectal Smooth Muscle	rectum
30	chr3:67704600-67705800	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr3:67704600-67706000	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr3:67704600-67706800	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr3:67705000-67705800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:67705000-67706600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr3:67705000-67706600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:67705200-67705800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:67705200-67705800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr3:67705200-67705800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr3:67705200-67705800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr3:67705200-67705800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:67705200-67705800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:67705200-67705800	Flanking Active TSS	Liver	Liver
43	chr3:67705200-67705800	Flanking Active TSS	Fetal Stomach	stomach
44	chr3:67705200-67705800	Flanking Active TSS	Pancreas	Pancrea
45	chr3:67705200-67705800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr3:67705200-67705800	Flanking Active TSS	Thymus	Thymus
47	chr3:67705200-67705800	Flanking Active TSS	Osteobl	bone
48	chr3:67705200-67706000	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr3:67705200-67706400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:67705200-67706400	Active TSS	Right Atrium	heart

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